In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step procedures, which can introduce inefficiencies, limit generalizability, and increase potential errors. To address these challenges, we present PhenoProfiler, an innovative model designed to efficiently and effectively extract morphological representations, enabling the elucidation of phenotypic changes induced by treatments. PhenoProfiler is designed as an end-to-end tool that processes whole-slide multi-channel images directly into low-dimensional quantitative representations, eliminating the extensive computational steps required by existing methods. It also includes a multi-objective learning module to enhance robustness, accuracy, and generalization in morphological representation learning. PhenoProfiler is rigorously evaluated on large-scale publicly available datasets, including over 230,000 whole-slide multi-channel images in end-to-end scenarios and more than 8.42 million single-cell images in non-end-to-end settings. Across these benchmarks, PhenoProfiler consistently outperforms state-of-the-art methods by up to 20%, demonstrating substantial improvements in both accuracy and robustness. Furthermore, PhenoProfiler uses a tailored phenotype correction strategy to emphasize relative phenotypic changes under treatments, facilitating the detection of biologically meaningful signals. UMAP visualizations of treatment profiles demonstrate PhenoProfiler ability to effectively cluster treatments with similar biological annotations, thereby enhancing interpretability. These findings establish PhenoProfiler as a scalable, generalizable, and robust tool for phenotypic learning.

Understanding information from visually rich documents remains a significant challenge for traditional Retrieval-Augmented Generation (RAG) methods. Existing benchmarks predominantly focus on image-based question answering (QA), overlooking the fundamental challenges of efficient retrieval, comprehension, and reasoning within dense visual documents. To bridge this gap, we introduce ViDoSeek, a novel dataset designed to evaluate RAG performance on visually rich documents requiring complex reasoning. Based on it, we identify key limitations in current RAG approaches: (i) purely visual retrieval methods struggle to effectively integrate both textual and visual features, and (ii) previous approaches often allocate insufficient reasoning tokens, limiting their effectiveness. To address these challenges, we propose ViDoRAG, a novel multi-agent RAG framework tailored for complex reasoning across visual documents. ViDoRAG employs a Gaussian Mixture Model (GMM)-based hybrid strategy to effectively handle multi-modal retrieval. To further elicit the model's reasoning capabilities, we introduce an iterative agent workflow incorporating exploration, summarization, and reflection, providing a framework for investigating test-time scaling in RAG domains. Extensive experiments on ViDoSeek validate the effectiveness and generalization of our approach. Notably, ViDoRAG outperforms existing methods by over 10% on the competitive ViDoSeek benchmark.

Domain Large Language Models (LLMs) are developed for domain-specific tasks based on general LLMs. But it still requires professional knowledge to facilitate the expertise for some domain-specific tasks. In this paper, we investigate into knowledge-intensive calculation problems. We find that the math problems to be challenging for LLMs, when involving complex domain-specific rules and knowledge documents, rather than simple formulations of terminologies. Therefore, we propose a pipeline to solve the domain-specific calculation problems with Knowledge-Intensive Programs Generator more effectively, named as KIPG. It generates knowledge-intensive programs according to the domain-specific documents. For each query, key variables are extracted, then outcomes which are dependent on domain knowledge are calculated with the programs. By iterative preference alignment, the code generator learns to improve the logic consistency with the domain knowledge. Taking legal domain as an example, we have conducted experiments to prove the effectiveness of our pipeline, and extensive analysis on the modules. We also find that the code generator is also adaptable to other domains, without training on the new knowledge.

While Large Language Models (LLMs) demonstrate impressive generation abilities, they frequently struggle when it comes to specialized domains due to their limited domain-specific knowledge. Studies on domain-specific LLMs resort to expanding the vocabulary before fine-tuning on domain-specific corpus, aiming to decrease the sequence length and enhance efficiency during decoding, without thoroughly investigating the results of vocabulary expansion to LLMs over different domains. Our pilot study reveals that expansion with only a subset of the entire vocabulary may lead to superior performance. Guided by the discovery, this paper explores how to identify a vocabulary subset to achieve the optimal results. We introduce VEGAD, an adaptive method that automatically identifies valuable words from a given domain vocabulary. Our method has been validated through experiments on three Chinese datasets, demonstrating its effectiveness. Additionally, we have undertaken comprehensive analyses of the method. The selection of a optimal subset for expansion has shown to enhance performance on both domain-specific tasks and general tasks, showcasing the potential of VEGAD.

The performance on general tasks decreases after Large Language Models (LLMs) are fine-tuned on domain-specific tasks, the phenomenon is known as Catastrophic Forgetting (CF). However, this paper presents a further challenge for real application of domain-specific LLMs beyond CF, called General Capabilities Integration (GCI), which necessitates the integration of both the general capabilities and domain knowledge within a single instance. The objective of GCI is not merely to retain previously acquired general capabilities alongside new domain knowledge, but to harmonize and utilize both sets of skills in a cohesive manner to enhance performance on domain-specific tasks. Taking legal domain as an example, we carefully design three groups of training and testing tasks without lacking practicability, and construct the corresponding datasets. To better incorporate general capabilities across domain-specific scenarios, we introduce ALoRA, which utilizes a multi-head attention module upon LoRA, facilitating direct information transfer from preceding tokens to the current one. This enhancement permits the representation to dynamically switch between domain-specific knowledge and general competencies according to the attention. Extensive experiments are conducted on the proposed tasks. The results exhibit the significance of our setting, and the effectiveness of our method.